We have studied the mechanisms of three protocellular functions studied using computational methods of molecular dynamics. These functions are (1) transport of ions and small, neutral solutes across membranes, (2) formation of photoactivated proton gradient that could drive chemical synthesis in the protocell, and (3) organization of small peptides necessary for catalytic activity. In all these processes, membranes play an essential role. They provide surfaces at which organic molecules concentrate and small peptides can organize into ordered, amphiphilic structures. Membranes also form a barrier to charged species that allows for retaining proton gradients. This gradients can be generated by a simple transmembrane proton pump consisting of a proton source and two acceptors has been considered. Its directionality is ensured by a ``gate-keeping'' mechanism involving a water molecule, conformational change of the primary acceptor or tautomerization of histidine. Transfer of ions across the barrier formed by protocellular walls is facilitated by the formation of deep, thinning defects in the membrane. In general, this work provides essential information about the origins and evolution of the earliest precursors of contemporary cells. We used the Computer Graphics Laboratory facilities, and the MidasPlus package in particular, to design the minimal, directional proton pump and visualize different conformations of peptides at the water-membrane interface.